Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001711.1 Hibiscus syriacus cultivar Beakdansim tig00003454_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4148933
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 13
Found at i:712326 original size:36 final size:36
Alignment explanation
Indices: 712261--712357 Score: 169
Period size: 36 Copynumber: 2.7 Consensus size: 36
712251 GTTGGTGATA
*
712261 ATATAGGCGTGAT-ATGGTGATGGAATATGGGGATG
1 ATATAGGCGTGATAATGGTGATGGACTATGGGGATG
*
712296 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATGGGGATG
712332 ATATAGGCGTGATAATGGTGATGGAC
1 ATATAGGCGTGATAATGGTGATGGAC
712358 AGATTGTATC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 13 0.22
36 46 0.78
ACGTcount: A:0.29, C:0.05, G:0.37, T:0.29
Consensus pattern (36 bp):
ATATAGGCGTGATAATGGTGATGGACTATGGGGATG
Found at i:716663 original size:19 final size:20
Alignment explanation
Indices: 716625--716674 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
716615 AAAATCCATT
*
716625 TGAAAATATATGATTTTTAA
1 TGAAAATACATGATTTTTAA
716645 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
716664 TGAAGATACAT
1 TGAAAATACAT
716675 ACTCTTGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:725607 original size:36 final size:35
Alignment explanation
Indices: 725556--725666 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
725546 TAAGATACTA
725556 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* *
725591 CCTATAACATCACCATCTTCCATTACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * * *
725626 CCTATATCATTACCTTCTTCTATCACCATTTCATG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
725661 CCTATA
1 CCTATA
725667 TAACCACCAA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
35 44 0.67
36 22 0.33
ACGTcount: A:0.27, C:0.36, G:0.04, T:0.33
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:726393 original size:26 final size:26
Alignment explanation
Indices: 726364--726424 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
726354 ATCCATTTCT
*
726364 TAACCTTTTCTATCCTAACCCTATCA
1 TAACCATTTCTATCCTAACCCTATCA
*
726390 TAACCATTTCTATCCTACCCCTATCA
1 TAACCATTTCTATCCTAACCCTATCA
726416 TAACCATTT
1 TAACCATTT
726425 GTAGACCCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (26 bp):
TAACCATTTCTATCCTAACCCTATCA
Found at i:729986 original size:35 final size:35
Alignment explanation
Indices: 729883--729988 Score: 122
Period size: 35 Copynumber: 3.0 Consensus size: 35
729873 ACTACCTAAA
*
729883 CATCACCATCTTCCATCACCATTTTCACGCCTATAA
1 CATCACCATCTTCCATCACCATTTT-ACGCCTATAT
* * ** *
729919 CATCACCATATTCCATTACCATTGAATGCCTATAT
1 CATCACCATCTTCCATCACCATTTTACGCCTATAT
* * *
729954 CATTACCATCTTCTATCACCATTTTACACCTATAT
1 CATCACCATCTTCCATCACCATTTTACGCCTATAT
729989 AACCACCAAT
Statistics
Matches: 56, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
35 35 0.62
36 21 0.38
ACGTcount: A:0.29, C:0.33, G:0.03, T:0.35
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATTTTACGCCTATAT
Found at i:730429 original size:19 final size:20
Alignment explanation
Indices: 730391--730441 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
730381 GAAACCCCTT
730391 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
730411 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
730430 TGAAGATACATG
1 TGAAAATACATG
730442 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:737218 original size:21 final size:19
Alignment explanation
Indices: 737194--737245 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
737184 GAAACCCCTT
737194 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGA-TTTT-AA
*
737215 TGAAAATACAAGATTTTAA
1 TGAAAATACATGATTTTAA
*
737234 TGAAGATACATG
1 TGAAAATACATG
737246 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:737237 original size:19 final size:21
Alignment explanation
Indices: 737194--737243 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
737184 GAAACCCCTT
*
737194 TGAAAATACATGATTTTTAAA
1 TGAAAATACAAGATTTTTAAA
737215 TGAAAATACAAGA-TTTT-AA
1 TGAAAATACAAGATTTTTAAA
*
737234 TGAAGATACA
1 TGAAAATACA
737244 TGCTCTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 12 0.44
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (21 bp):
TGAAAATACAAGATTTTTAAA
Found at i:741336 original size:19 final size:21
Alignment explanation
Indices: 741293--741344 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
741283 GAAACCCCTT
741293 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
741314 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
741333 TGAAGATACATG
1 TGAAAATACATG
741345 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:743151 original size:13 final size:11
Alignment explanation
Indices: 743110--743194 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
743100 ACAATCTGTC
743110 CATCACCATTAT
1 CATCACCA-TAT
*
743122 CA-CGCCTATAT
1 CATCACC-ATAT
743133 CATCACCATAGT
1 CATCACCATA-T
743145 CCATCACCATTAT
1 -CATCACCA-TAT
*
743158 CATGC-CTATAT
1 CAT-CACCATAT
743169 CATCACCATATT
1 CATCACCATA-T
743181 CCATCACCATAT
1 -CATCACCATAT
743193 CA
1 CA
743195 CGCCTATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 1 0.02
11 23 0.38
12 14 0.23
13 20 0.33
14 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:743154 original size:36 final size:36
Alignment explanation
Indices: 743107--743211 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
743097 GATACAATCT
743107 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
743143 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
743179 TTCCATCACCA-TATCACGCCTATTTTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
743212 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 19 0.30
36 45 0.70
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:745039 original size:9 final size:9
Alignment explanation
Indices: 745019--745050 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
745009 TTTGATTTCA
745019 TCTTTT-TT
1 TCTTTTCTT
745027 TCTTTTCTT
1 TCTTTTCTT
745036 TCTTTTCTT
1 TCTTTTCTT
745045 TCTTTT
1 TCTTTT
745051 GCACTCCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.26
9 17 0.74
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TCTTTTCTT
Found at i:747101 original size:36 final size:35
Alignment explanation
Indices: 747050--747160 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
747040 TAATATACTA
747050 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* *
747085 CCTATAACATCACCATCTTCCATTACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * * *
747120 CCTATATCATTACCATATTCTATCACCATTTCATG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
747155 CCTATA
1 CCTATA
747161 TAACCACCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
35 44 0.67
36 22 0.33
ACGTcount: A:0.29, C:0.35, G:0.04, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:747750 original size:127 final size:127
Alignment explanation
Indices: 747524--747783 Score: 502
Period size: 127 Copynumber: 2.0 Consensus size: 127
747514 TTATATTATA
747524 TTTACTCATTTATGCACTATATATTATTATGACCATACTTTTGCATCTTAAACTATGCTTGAATA
1 TTTACTCATTTATGCACTATATATTATTATGACCATACTTTTGCATCTTAAACTATGCTTGAATA
*
747589 ATCATATGTTATCATTCACTTGTAACTATATGATTTTCATGCATAACATATGTTTTCACATC
66 ATCATATGTTATCATTCACTTGCAACTATATGATTTTCATGCATAACATATGTTTTCACATC
*
747651 TTTACTCATTTATGCACTATATATTATTATGAGCATACTTTTGCATCTTAAACTATGCTTGAATA
1 TTTACTCATTTATGCACTATATATTATTATGACCATACTTTTGCATCTTAAACTATGCTTGAATA
747716 ATCATATGTTATCATTCACTTGCAACTATATGATTTTCATGCATAACATATGTTTTCACATC
66 ATCATATGTTATCATTCACTTGCAACTATATGATTTTCATGCATAACATATGTTTTCACATC
747778 TTTACT
1 TTTACT
747784 TAGCTTTATA
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 131 1.00
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.44
Consensus pattern (127 bp):
TTTACTCATTTATGCACTATATATTATTATGACCATACTTTTGCATCTTAAACTATGCTTGAATA
ATCATATGTTATCATTCACTTGCAACTATATGATTTTCATGCATAACATATGTTTTCACATC
Found at i:748769 original size:19 final size:20
Alignment explanation
Indices: 748745--748790 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
748735 CGGCCAAGAG
*
748745 CATGTATCTTAAT-TAAAAT
1 CATGTATCTTAATCAAAAAT
* *
748764 CATGTATTTTCATCAAAAAT
1 CATGTATCTTAATCAAAAAT
748784 CATGTAT
1 CATGTAT
748791 TTTCAAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (20 bp):
CATGTATCTTAATCAAAAAT
Found at i:749232 original size:19 final size:20
Alignment explanation
Indices: 749208--749256 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
749198 TATCATTTCT
749208 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
749227 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
749247 -TATTATTATT
1 TTATT-TTATT
749257 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:749550 original size:19 final size:18
Alignment explanation
Indices: 749511--749568 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
749501 TTGGAGTGCA
*
749511 AAAAGAA-AGAAAAAGAT
1 AAAAGAAGAGAAAAAGAG
*
749528 AAAAGAAGAGAAAAATTAG
1 AAAAGAAGAGAAAAA-GAG
*
749547 AAAAGAAGA-AAAGAAAAG
1 AAAAGAAGAGAAA-AAGAG
749565 AAAA
1 AAAA
749569 AGAGAAGTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 7 0.20
18 16 0.46
19 12 0.34
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (18 bp):
AAAAGAAGAGAAAAAGAG
Found at i:749569 original size:19 final size:20
Alignment explanation
Indices: 749514--749571 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
749504 GAGTGCAAAA
749514 AGAAAGAAAAAGATAAAAGAAG
1 AGAAAG-AAAAGA-AAAAGAAG
*
749536 AGAAA-AATTAG-AAAAGAAG
1 AGAAAGAA-AAGAAAAAGAAG
749555 A-AAAGAAAAGAAAAAGA
1 AGAAAGAAAAGAAAAAGA
749572 GAAGTTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 17 0.55
20 2 0.06
21 2 0.06
22 5 0.16
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (20 bp):
AGAAAGAAAAGAAAAAGAAG
Found at i:750893 original size:24 final size:25
Alignment explanation
Indices: 750839--750903 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
750829 ACGTTCCAAC
* *
750839 AGATAT-ACCACTTGAAGTTCAAAA
1 AGATATGATCACTTGAAGTGCAAAA
750863 AGATATG-TCACTTGAAGTGCAAAA
1 AGATATGATCACTTGAAGTGCAAAA
*
750887 AGTTATGATCA-TTGAAG
1 AGATATGATCACTTGAAG
750904 CTCCAAGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 33 0.92
25 3 0.08
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (25 bp):
AGATATGATCACTTGAAGTGCAAAA
Found at i:751973 original size:30 final size:31
Alignment explanation
Indices: 751937--751996 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
751927 CTTAGCTTTA
**
751937 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
751967 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
751997 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:752917 original size:19 final size:20
Alignment explanation
Indices: 752893--752943 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
752883 CGGCCAAGAG
* *
752893 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
752912 CATGTATTTTCATAAAAAAT
1 CATGTATTTTCATAAAAAAT
752932 CATGTATTTTCA
1 CATGTATTTTCA
752944 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:753380 original size:19 final size:20
Alignment explanation
Indices: 753356--753404 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
753346 TATCCTTTCT
753356 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
753375 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
753395 -TATTATTATT
1 TTATT-TTATT
753405 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:761802 original size:15 final size:14
Alignment explanation
Indices: 761758--761805 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 14
761748 TTGGAAATAA
761758 GAAATGAAAGAAAT
1 GAAATGAAAGAAAT
761772 GGAAATTGATAAGAAAT
1 -GAAA-TGA-AAGAAAT
761789 GAAATGGAAAGAAAT
1 GAAAT-GAAAGAAAT
761804 GA
1 GA
761806 TATCAAGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 14 0.47
16 9 0.30
17 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (14 bp):
GAAATGAAAGAAAT
Found at i:761802 original size:26 final size:24
Alignment explanation
Indices: 761754--761807 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 24
761744 TTAATTGGAA
761754 ATAAGAAATGAAAGAAATGGAAATTG
1 ATAAGAAATGAAAGAAA-GGAAA-TG
761780 ATAAGAAATGAAATGGAAA-GAAATG
1 ATAAGAAATGAAA--GAAAGGAAATG
761805 ATA
1 ATA
761808 TCAAGGTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 5 0.19
26 17 0.65
28 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (24 bp):
ATAAGAAATGAAAGAAAGGAAATG
Found at i:768677 original size:27 final size:28
Alignment explanation
Indices: 768625--768689 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
768615 GAAGAAAATC
*
768625 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
768653 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTCAAAAAGA
768680 AGAAAAGAAA
1 AGAAAAGAAA
768690 AGAAAGAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.62, C:0.11, G:0.17, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:770022 original size:24 final size:21
Alignment explanation
Indices: 769988--770030 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
769978 TCCACAAGAC
*
769988 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
770010 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
770031 AGAAAGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:771588 original size:13 final size:12
Alignment explanation
Indices: 771529--771585 Score: 73
Period size: 12 Copynumber: 4.8 Consensus size: 12
771519 TGGACTAAAG
771529 GTAGCT-GGA-A
1 GTAGCTGGGAGA
771539 GTAGCTGGGAGA
1 GTAGCTGGGAGA
*
771551 GTAGCTGAAGAGA
1 GTAGCTG-GGAGA
771564 GGTAGCTGGGAGA
1 -GTAGCTGGGAGA
771577 GTAGCTGGG
1 GTAGCTGGG
771586 GAGCTAACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
10 6 0.15
11 3 0.07
12 17 0.41
13 8 0.20
14 7 0.17
ACGTcount: A:0.26, C:0.09, G:0.47, T:0.18
Consensus pattern (12 bp):
GTAGCTGGGAGA
Found at i:773715 original size:18 final size:17
Alignment explanation
Indices: 773666--773719 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 17
773656 GAGTTGTAAG
773666 TTATCTTCATTTTTCTTA
1 TTAT-TTCATTTTTCTTA
*
773684 CTATTTCA-TTTTCTTA
1 TTATTTCATTTTTCTTA
*
773700 TTCTTTCATCTTTTCTTA
1 TTATTTCAT-TTTTCTTA
773718 TT
1 TT
773720 TTCAATACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 14 0.45
17 4 0.13
18 13 0.42
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTCATTTTTCTTA
Found at i:781592 original size:15 final size:15
Alignment explanation
Indices: 781555--781600 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
781545 TGATAATTAA
781555 GAAATGGAAAGTAAATG
1 GAAATGGAAAG--AATG
*
781572 GAAATGGAAAGAATT
1 GAAATGGAAAGAATG
*
781587 GAAATGGATAGAAT
1 GAAATGGAAAGAAT
781601 AGTTATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 16 0.59
17 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.28, T:0.20
Consensus pattern (15 bp):
GAAATGGAAAGAATG
Found at i:781779 original size:13 final size:12
Alignment explanation
Indices: 781760--781845 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
781750 AAATAGGCGT
781760 GATATGGTGATG
1 GATATGGTGATG
781772 GAATATGGTGAT-
1 G-ATATGGTGATG
*
781784 GATATAGGCG-T-
1 GATAT-GGTGATG
781795 GATAATGGTGATG
1 GAT-ATGGTGATG
781808 GACTATGGTGAT-
1 GA-TATGGTGATG
*
781820 GATATAGGCG-T-
1 GATAT-GGTGATG
781831 GATAATGGTGATG
1 GAT-ATGGTGATG
781844 GA
1 GA
781846 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:781815 original size:36 final size:36
Alignment explanation
Indices: 781742--781846 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
781732 ATTTATAAGT
* * *
781742 TGGTGATAAAATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
781777 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
781813 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
781847 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:785797 original size:14 final size:14
Alignment explanation
Indices: 785780--785818 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
785770 TTGCTTTTGA
785780 TTTTCTTCTTTTTC
1 TTTTCTTCTTTTTC
*
785794 TTTTCTT-TCTTTTG
1 TTTTCTTCT-TTTTC
785808 TTTTCTTCTTT
1 TTTTCTTCTTT
785819 CTTGTTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTTCTTCTTTTTC
Found at i:785834 original size:28 final size:28
Alignment explanation
Indices: 785762--785818 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
785752 ACTTGCTTCA
785762 CTTTTCTTTTGCTTTTGATTTTCTTCTTTTT
1 CTTTTC-TTT-CTTTTGATTTTCTTC-TTTT
785793 CTTTTCTTTCTTTTG-TTTTCTTCTTT
1 CTTTTCTTTCTTTTGATTTTCTTCTTT
785819 CTTGTTGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 3 0.12
28 8 0.31
29 6 0.23
30 3 0.12
31 6 0.23
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (28 bp):
CTTTTCTTTCTTTTGATTTTCTTCTTTT
Found at i:786251 original size:13 final size:12
Alignment explanation
Indices: 786232--786317 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
786222 AAATAGGCGT
786232 GATATGGTGATG
1 GATATGGTGATG
786244 GAATATGGTGAT-
1 G-ATATGGTGATG
*
786256 GATATAGGCG-T-
1 GATAT-GGTGATG
786267 GATAATGGTGATG
1 GAT-ATGGTGATG
786280 GACTATGGTGAT-
1 GA-TATGGTGATG
*
786292 GATATAGGCG-T-
1 GATAT-GGTGATG
786303 GATAATGGTGATG
1 GAT-ATGGTGATG
786316 GA
1 GA
786318 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:786287 original size:36 final size:36
Alignment explanation
Indices: 786214--786318 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
786204 ATTTATAAGT
* * *
786214 TGGTGATAAAATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
786249 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
786285 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
786319 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:789787 original size:13 final size:13
Alignment explanation
Indices: 789769--789830 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
789759 AGATACTATT
789769 TCCATCACCATAA
1 TCCATCACCATAA
* *
789782 TCCATCTTCCATTA
1 TCCATC-ACCATAA
789796 T-CA-CACC-TATA
1 TCCATCACCATA-A
*
789807 T-CATCACCATAG
1 TCCATCACCATAA
789819 TCCATCACCATA
1 TCCATCACCATA
789831 TCACACCTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
10 1 0.03
11 6 0.15
12 6 0.15
13 20 0.51
14 6 0.15
ACGTcount: A:0.32, C:0.37, G:0.02, T:0.29
Consensus pattern (13 bp):
TCCATCACCATAA
Found at i:789840 original size:35 final size:37
Alignment explanation
Indices: 789771--789846 Score: 120
Period size: 35 Copynumber: 2.1 Consensus size: 37
789761 ATACTATTTC
*
789771 CATCACCATAATCCATCTTCCATTATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
789808 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
789843 CATC
1 CATC
789847 CTCAAATTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 18 0.49
36 3 0.08
37 16 0.43
ACGTcount: A:0.33, C:0.37, G:0.01, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:789844 original size:11 final size:11
Alignment explanation
Indices: 789771--789846 Score: 57
Period size: 11 Copynumber: 6.4 Consensus size: 11
789761 ATACTATTTC
789771 CATCACCATAAT
1 CATCACCAT-AT
*
789783 CCATCTTCCATTAT
1 -CATC-ACCA-TAT
789797 CA-CACCTATAT
1 CATCACC-ATAT
789808 CATCACCATAGT
1 CATCACCATA-T
789820 CCATCACCATAT
1 -CATCACCATAT
789832 CA-CACCTATAT
1 CATCACC-ATAT
789843 CATC
1 CATC
789847 CTCAAATTCT
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
10 4 0.08
11 18 0.34
12 9 0.17
13 16 0.30
14 5 0.09
15 1 0.02
ACGTcount: A:0.33, C:0.37, G:0.01, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:790326 original size:14 final size:15
Alignment explanation
Indices: 790292--790338 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
790282 AATTTAGAGT
790292 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
790307 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
790321 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
790338 G
1 G
790339 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:795526 original size:11 final size:11
Alignment explanation
Indices: 795476--795532 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
795466 GATCTTCCAT
795476 TATCA-CACCTA
1 TATCATCACC-A
795487 TATCATCACCA
1 TATCATCACCA
*
795498 TAGTCCATTACCA
1 TA-T-CATCACCA
795511 TATCA-CACCTA
1 TATCATCACC-A
795522 TATCATCACCA
1 TATCATCACCA
795533 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 3 0.08
11 17 0.44
12 10 0.26
13 9 0.23
ACGTcount: A:0.35, C:0.35, G:0.02, T:0.28
Consensus pattern (11 bp):
TATCATCACCA
Found at i:801439 original size:15 final size:16
Alignment explanation
Indices: 801388--801440 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
801378 AGATAGTGAA
801388 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
801405 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
801422 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
801437 ATAA
1 ATAA
801441 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:813350 original size:23 final size:23
Alignment explanation
Indices: 813324--813380 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
813314 GCATAATTAT
813324 CATTCATTTTATCAGCTCCTATG
1 CATTCATTTTATCAGCTCCTATG
813347 CATTCATTTTATCAGCTCCTATG
1 CATTCATTTTATCAGCTCCTATG
*
813370 CATTAATTTTA
1 CATTCATTTTA
813381 GCACTTAGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.46
Consensus pattern (23 bp):
CATTCATTTTATCAGCTCCTATG
Found at i:815084 original size:14 final size:14
Alignment explanation
Indices: 815065--815096 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
815055 GAAGGTTGTG
*
815065 AAGTGACTTGTGTA
1 AAGTGACTTGAGTA
815079 AAGTGACTTGAGTA
1 AAGTGACTTGAGTA
815093 AAGT
1 AAGT
815097 TCTCTAGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (14 bp):
AAGTGACTTGAGTA
Found at i:824915 original size:23 final size:23
Alignment explanation
Indices: 824857--824925 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 23
824847 GAATTGTTGA
* *
824857 TGAGTGCTTCCAACTTTCTTTTTTTT
1 TGAGTGCTTTCAA-TTTC--TTCTTT
824883 TCGAGTGCTTTCAATTTCTTCTTT
1 T-GAGTGCTTTCAATTTCTTCTTT
* *
824907 TGAGTGCTTTTATTTTCTT
1 TGAGTGCTTTCAATTTCTT
824926 TTCTGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 16 0.42
24 6 0.16
26 5 0.13
27 11 0.29
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (23 bp):
TGAGTGCTTTCAATTTCTTCTTT
Found at i:835976 original size:30 final size:31
Alignment explanation
Indices: 835937--835996 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
835927 ACATGCTGCC
**
835937 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
835968 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
835997 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:837067 original size:24 final size:24
Alignment explanation
Indices: 837031--837091 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
837021 AACTTGGATA
*
837031 TTCAA-TGATCATATCTTTTGACAC
1 TTCAAGTGA-CATATCTTTTGAAAC
*
837055 TTCAAGTGACATATCTTTTTAAAC
1 TTCAAGTGACATATCTTTTGAAAC
*
837079 TTCAAGTGGCATA
1 TTCAAGTGACATA
837092 ACTGTTGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (24 bp):
TTCAAGTGACATATCTTTTGAAAC
Found at i:838385 original size:19 final size:19
Alignment explanation
Indices: 838363--838418 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
838353 TTTGAACTTC
838363 TCTTTTTCTTTTCTTTTCT
1 TCTTTTTCTTTTCTTTTCT
*
838382 TC-TTTTCTAATTT-TTCTCT
1 TCTTTTTCT--TTTCTTTTCT
838401 TCTTTTCTCTTTTTCTTT
1 TCTTTT-TC-TTTTCTTT
838419 CTTTTTGCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 6 0.21
19 9 0.31
20 9 0.31
21 4 0.14
22 1 0.03
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (19 bp):
TCTTTTTCTTTTCTTTTCT
Found at i:839172 original size:19 final size:20
Alignment explanation
Indices: 839133--839181 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
839123 AACCCCTTTA
*
839133 AAAATACATGATTTTTGATG
1 AAAATACATGATTTTTAATG
839153 AAAATACATGA-TTTTAATG
1 AAAATACATGATTTTTAATG
*
839172 AAGATACATG
1 AAAATACATG
839182 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
AAAATACATGATTTTTAATG
Found at i:840117 original size:30 final size:31
Alignment explanation
Indices: 840078--840137 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
840068 ACATGCTGCC
**
840078 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
840109 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
840138 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:847103 original size:19 final size:18
Alignment explanation
Indices: 847059--847111 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 18
847049 TTGAAACCCC
847059 TTTGAAAATACATGATTT
1 TTTGAAAATACATGATTT
847077 TTGATGAAAATACATGATTT
1 TT--TGAAAATACATGATTT
*
847097 TATTGAAGATACATG
1 T-TTGAAAATACATG
847112 CTCTTGGCCG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 2 0.06
19 11 0.35
20 17 0.55
21 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (18 bp):
TTTGAAAATACATGATTT
Found at i:848034 original size:30 final size:31
Alignment explanation
Indices: 847995--848054 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
847985 ACATGCTTCC
**
847995 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
848026 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
848055 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:848482 original size:19 final size:20
Alignment explanation
Indices: 848458--848508 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
848448 CGGCCAAGAG
*
848458 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
848477 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
848497 CATGTATTTTCA
1 CATGTATTTTCA
848509 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:850210 original size:13 final size:13
Alignment explanation
Indices: 850192--850225 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
850182 GATGATGGTC
850192 TTGATGAAGGATG
1 TTGATGAAGGATG
*
850205 TTGATGATGGATG
1 TTGATGAAGGATG
*
850218 ATGATGAA
1 TTGATGAA
850226 ATGGCAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TTGATGAAGGATG
Found at i:852663 original size:24 final size:23
Alignment explanation
Indices: 852636--852697 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
852626 GAAAGCAAGA
852636 AAAAAAATCAGAAAAG-AAGCACT
1 AAAAAAAT-AGAAAAGAAAGCACT
* *
852659 GAAAAAGA-AGAAATTGAAAGCACT
1 -AAAAAAATAGAAA-AGAAAGCACT
852683 AAAAAAATAGAAAAG
1 AAAAAAATAGAAAAG
852698 TTGGAAGCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
22 5 0.16
23 8 0.26
24 18 0.58
ACGTcount: A:0.66, C:0.08, G:0.16, T:0.10
Consensus pattern (23 bp):
AAAAAAATAGAAAAGAAAGCACT
Found at i:861581 original size:47 final size:47
Alignment explanation
Indices: 861527--861620 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 47
861517 GGCATCTCCC
*
861527 TTGGCCGAATGGTGA-TG-CTTGTTCATCTTGGCGCCAAATGCTTCTCT
1 TTGGCCGAATGGTGAGTGCCTCG-TCATCTTGGCGCCAAATG-TTCTCT
* *
861574 TTGGCCGATTGGTGATGTGCCTCGTCATGTTGGCGCCAAATGTTCTC
1 TTGGCCGAATGGTGA-GTGCCTCGTCATCTTGGCGCCAAATGTTCTC
861621 ATGTGCATAG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
47 14 0.34
48 5 0.12
49 19 0.46
50 3 0.07
ACGTcount: A:0.14, C:0.23, G:0.28, T:0.35
Consensus pattern (47 bp):
TTGGCCGAATGGTGAGTGCCTCGTCATCTTGGCGCCAAATGTTCTCT
Found at i:876121 original size:16 final size:16
Alignment explanation
Indices: 876100--876132 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
876090 TTCTGCCACC
876100 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
876116 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
876132 T
1 T
876133 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:879358 original size:16 final size:16
Alignment explanation
Indices: 879337--879370 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
879327 TGCATTCTGC
*
879337 CACATATGTTAGAATG
1 CACATATATTAGAATG
879353 CACATATATTAGAATG
1 CACATATATTAGAATG
879369 CA
1 CA
879371 AATGAGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (16 bp):
CACATATATTAGAATG
Found at i:880083 original size:24 final size:23
Alignment explanation
Indices: 880055--880114 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
880045 ACTTTTGTTT
880055 CTTTCTTTTTCTTCTTTTCGAGTG
1 CTTTCTTTTTCTTCTTTT-GAGTG
**
880079 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCTTTTTCTTCTTTTGAGTG
880102 CTTT-TATTTTCTT
1 CTTTCT-TTTTCTT
880115 TGCTGATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.08, C:0.18, G:0.10, T:0.63
Consensus pattern (23 bp):
CTTTCTTTTTCTTCTTTTGAGTG
Found at i:880104 original size:23 final size:24
Alignment explanation
Indices: 880062--880114 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
880052 TTTCTTTCTT
880062 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
880086 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
880109 TTTCTT
1 TTTCTT
880115 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:887290 original size:13 final size:12
Alignment explanation
Indices: 887272--887306 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
887262 CTTGCACTTC
887272 TTTTTTTGTATTT
1 TTTTTTTGT-TTT
887285 TTTTTTTGTTTT
1 TTTTTTTGTTTT
*
887297 TGTTTTTGTT
1 TTTTTTTGTT
887307 GTTGCTCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:890906 original size:15 final size:16
Alignment explanation
Indices: 890880--890912 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
890870 TTGCACTTCT
*
890880 TTTTTGTATTTTTTTG
1 TTTTTGTATTTTGTTG
890896 TTTTTGT-TTTTGTTG
1 TTTTTGTATTTTGTTG
890911 TT
1 TT
890913 GCTCGTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (16 bp):
TTTTTGTATTTTGTTG
Found at i:901569 original size:11 final size:11
Alignment explanation
Indices: 901519--901571 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 11
901509 TATCACGCCT
901519 ATATCATCACC
1 ATATCATCACC
901530 ATAGTCCATCACC
1 ATA-T-CATCACC
*
901543 ATTATCA-CGCC
1 A-TATCATCACC
901554 TATATCATCACC
1 -ATATCATCACC
901566 ATATCA
1 ATATCA
901572 CGCCTATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
11 17 0.49
12 7 0.20
13 9 0.26
14 2 0.06
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.28
Consensus pattern (11 bp):
ATATCATCACC
Found at i:901570 original size:22 final size:23
Alignment explanation
Indices: 901536--901588 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
901526 CACCATAGTC
901536 CATCACCATTATCACGCCTATAT
1 CATCACCATTATCACGCCTATAT
901559 CATCACCA-TATCACGCCTATAT
1 CATCACCATTATCACGCCTATAT
*
901581 TATCACCA
1 CATCACCA
901589 ACTTATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (23 bp):
CATCACCATTATCACGCCTATAT
Found at i:901586 original size:36 final size:36
Alignment explanation
Indices: 901497--901568 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
901487 GATACAATCT
*
901497 GTCCACCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
901533 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
901569 TCACGCCTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.31, C:0.38, G:0.06, T:0.26
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:903452 original size:13 final size:11
Alignment explanation
Indices: 903411--903495 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
903401 ACAATCTGTC
903411 CATCACCATTAT
1 CATCACCA-TAT
*
903423 CA-CGCCTATAT
1 CATCACC-ATAT
903434 CATCACCATAGT
1 CATCACCATA-T
903446 CCATCACCATTAT
1 -CATCACCA-TAT
*
903459 CA-CGCCTATAT
1 CATCACC-ATAT
903470 CATCACCATATT
1 CATCACCATA-T
903482 CCATCACCATAT
1 -CATCACCATAT
903494 CA
1 CA
903496 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:903455 original size:36 final size:36
Alignment explanation
Indices: 903408--903512 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
903398 GATACAATCT
903408 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
903444 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
903480 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
903513 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:903983 original size:14 final size:15
Alignment explanation
Indices: 903952--903993 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
903942 TTTGGAGTGC
903952 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
903967 AAAAG-AAGAATA-A
1 AAAAGAAAGAAAAGA
903980 AAAAGCAAAGAAAA
1 AAAAG-AAAGAAAA
903994 AGTGAAGCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.26
14 6 0.26
15 11 0.48
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:908306 original size:36 final size:36
Alignment explanation
Indices: 908259--908363 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
908249 GATATAATCT
908259 GTCCATCACCATTATCACGCCTATATTATCACCATA
1 GTCCATCACCATTATCACGCCTATATTATCACCATA
*
908295 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATTATCACCATA
* * *
908331 TTCGATCACCA-TATGACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATTATCACCA
908364 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 20 0.31
36 44 0.69
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATTATCACCATA
Found at i:908819 original size:9 final size:9
Alignment explanation
Indices: 908805--908831 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
908795 TTTGGAGTGC
908805 AAAAGAAAA
1 AAAAGAAAA
908814 AAAAGAAAA
1 AAAAGAAAA
908823 AAAAGAAAA
1 AAAAGAAAA
908832 TCAAAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:912841 original size:11 final size:11
Alignment explanation
Indices: 912772--912843 Score: 51
Period size: 11 Copynumber: 6.2 Consensus size: 11
912762 ACAATCTGTC
912772 CATCACCATTAT
1 CATCACCA-TAT
*
912784 CA-CGCCTATAT
1 CATCACC-ATAT
912795 CATCACCATAGT
1 CATCACCATA-T
912807 CCATCACCAT-T
1 -CATCACCATAT
912818 -ATCACGCATATAT
1 CATCAC-C--ATAT
912831 CATCACCATAT
1 CATCACCATAT
912842 CA
1 CA
912844 CGCCTATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 19
0.70 0.03 0.27
Matches are distributed among these distances:
9 5 0.10
10 1 0.02
11 18 0.37
12 9 0.18
13 11 0.22
14 5 0.10
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:912842 original size:22 final size:23
Alignment explanation
Indices: 912808--912860 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
912798 CACCATAGTC
912808 CATCACCATTATCACGCATATAT
1 CATCACCATTATCACGCATATAT
*
912831 CATCACCA-TATCACGCCTATAT
1 CATCACCATTATCACGCATATAT
*
912853 TATCACCA
1 CATCACCA
912861 ACTTATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.28
Consensus pattern (23 bp):
CATCACCATTATCACGCATATAT
Found at i:912858 original size:36 final size:36
Alignment explanation
Indices: 912769--912840 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
912759 GATACAATCT
*
912769 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCATATATCATCACCATA
912805 GTCCATCACCATTATCACGCATATATCATCACCATA
1 GTCCATCACCATTATCACGCATATATCATCACCATA
912841 TCACGCCTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.35, G:0.06, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCATATATCATCACCATA
Found at i:914249 original size:24 final size:23
Alignment explanation
Indices: 914194--914262 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
914184 TCTTCCACCA
** *
914194 AAGCTCTGATTACTGCTTGATATG
1 AAGCTCTGA-TACCACTTGATGTG
*
914218 AGGCTCTGATACCACTTGATGTG
1 AAGCTCTGATACCACTTGATGTG
*
914241 AAGCTTCTGATGCCACTTGATG
1 AAGC-TCTGATACCACTTGATG
914263 CAATGCACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.37
24 24 0.63
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (23 bp):
AAGCTCTGATACCACTTGATGTG
Found at i:916010 original size:24 final size:25
Alignment explanation
Indices: 915978--916038 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
915968 CTTGGCTTGC
915978 TTTC-TCTTTTGAATTTCTT-TTCT
1 TTTCTTCTTTTGAATTTCTTCTTCT
* *
916001 TTTCTTCTTTTCTGATTTTTTTCTTCT
1 TTTCTTC-TTT-TGAATTTCTTCTTCT
*
916028 TTTCTTGTTTT
1 TTTCTTCTTTT
916039 TTTCTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 4 0.13
24 2 0.06
25 4 0.13
26 11 0.35
27 10 0.32
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (25 bp):
TTTCTTCTTTTGAATTTCTTCTTCT
Found at i:916038 original size:16 final size:17
Alignment explanation
Indices: 916000--916046 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
915990 ATTTCTTTTC
*
916000 TTTTCTTCTTTTCTGATTT
1 TTTTCTTCTTTTC--ATTG
916019 TTTTCTTCTTTTC-TTG
1 TTTTCTTCTTTTCATTG
*
916035 TTTTTTTCTTTT
1 TTTTCTTCTTTT
916047 TTTTTTGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 13 0.50
19 13 0.50
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (17 bp):
TTTTCTTCTTTTCATTG
Found at i:916049 original size:19 final size:19
Alignment explanation
Indices: 915991--916048 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
915981 CTCTTTTGAA
*
915991 TTTCTT-TTCTTTTCTTCT
1 TTTCTTGTTTTTTTCTTCT
916009 TTTC-TGATTTTTTTCTTCT
1 TTTCTTG-TTTTTTTCTTCT
916028 TTTCTTGTTTTTTTCTT-T
1 TTTCTTGTTTTTTTCTTCT
916046 TTT
1 TTT
916049 TTTTGCACTC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 1 0.03
18 8 0.22
19 25 0.69
20 2 0.06
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTCTTGTTTTTTTCTTCT
Found at i:917708 original size:2 final size:2
Alignment explanation
Indices: 917701--917726 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
917691 ATGAAATAAC
917701 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
917727 GTGTGTAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:918827 original size:19 final size:20
Alignment explanation
Indices: 918803--918848 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
918793 CGGCCAAGAG
918803 CATGTATCGTCATT-AAAAT
1 CATGTATCGTCATTAAAAAT
**
918822 CATGTATTTTCATTAAAAAT
1 CATGTATCGTCATTAAAAAT
918842 CATGTAT
1 CATGTAT
918849 TTTCAAAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (20 bp):
CATGTATCGTCATTAAAAAT
Found at i:918842 original size:20 final size:19
Alignment explanation
Indices: 918812--918853 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
918802 GCATGTATCG
918812 TCATTAAAATCATGTATTT
1 TCATTAAAATCATGTATTT
918831 TCATTAAAAATCATGTATTT
1 TCATT-AAAATCATGTATTT
918851 TCA
1 TCA
918854 AAGGGGTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (19 bp):
TCATTAAAATCATGTATTT
Found at i:919360 original size:6 final size:6
Alignment explanation
Indices: 919349--919381 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
919339 ATCTCAATTC
*
919349 TTTCCA TTTCCA TTTCCA TTTCCT TTTCC- TTTC
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTC
919382 TTAATTATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.09, C:0.33, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTCCA
Found at i:921655 original size:25 final size:25
Alignment explanation
Indices: 921621--921678 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
921611 GGGGAAGAAT
*
921621 TTCAGCCAAGATACATTCATGAAAA
1 TTCATCCAAGATACATTCATGAAAA
* *
921646 TTTATCCAAGATACATTCATGAACA
1 TTCATCCAAGATACATTCATGAAAA
921671 TTCATCCA
1 TTCATCCA
921679 TAGAAGACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (25 bp):
TTCATCCAAGATACATTCATGAAAA
Found at i:922643 original size:14 final size:14
Alignment explanation
Indices: 922626--922655 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
922616 TCATTATTTC
922626 AACCGATCCTAAGG
1 AACCGATCCTAAGG
922640 AACCGATCCTAAGG
1 AACCGATCCTAAGG
922654 AA
1 AA
922656 GTCTTCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (14 bp):
AACCGATCCTAAGG
Found at i:932169 original size:21 final size:21
Alignment explanation
Indices: 932129--932172 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
932119 AAGAAAGCAA
*
932129 AAGGAAAGAAAAAATCAAAGC
1 AAGGAAAGAAAAAATAAAAGC
**
932150 AAGGAAAGAAAAGTTAAAAGC
1 AAGGAAAGAAAAAATAAAAGC
932171 AA
1 AA
932173 AGGTTGTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.66, C:0.07, G:0.20, T:0.07
Consensus pattern (21 bp):
AAGGAAAGAAAAAATAAAAGC
Found at i:932885 original size:525 final size:525
Alignment explanation
Indices: 931895--932942 Score: 2019
Period size: 525 Copynumber: 2.0 Consensus size: 525
931885 CATATTTAAC
931895 CATTTCTTTAAAGCCTTTTTATTTCAGGAACACTTGCTGTCTTTCTAGGTCCTACAATCAAAGTG
1 CATTTCTTTAAAGCCTTTTTATTTCAGGAACACTTGCTGTCTTTCTAGGTCCTACAATCAAAGTG
931960 TAAGTCTTACCTCACCAAGTGGTGTAGGGCGTGCTTATATCATGTGGTAATCAGAACTAAGGTGG
66 TAAGTCTTACCTCACCAAGTGGTGTAGGGCGTGCTTATATCATGTGGTAATCAGAACTAAGGTGG
932025 AAGGAAGCAAGTTATGAAGTGTTGAGTCATCGAAACAAGTAAAAACAAAAGGAAAAAGAAGTGTT
131 AAGGAAGCAAGTTATGAAGTGTTGAGTCATCGAAACAAGTAAAAACAAAAGGAAAAAGAAGTGTT
*
932090 ATTCAAAAATCCTTGAAGAAACGTGAAAAAAGAAAGCAAAAGGAAAGAAAAAATCAAAGCAAGGA
196 ATTCAAAAATCCTTGAAGAAACGTGAAAAAAGAAAGCAAAAGGAAAGAAAAAATCAAAGCAAGAA
932155 AAGAAAAGTTAAAAGCAAAGGTTGTTTCATACATGAACAAGTGCCAACAAGCCTAAAGTTGTTTT
261 AAGAAAAGTTAAAAGCAAAGGTTGTTTCATACATGAACAAGTGCCAACAAGCCTAAAGTTGTTTT
932220 CAACACTTTGATTATGGCTAGGGAAGGTTATTAGTGTCTTGTAGTAAGAACCCCTTTCCTTCTAT
326 CAACACTTTGATTATGGCTAGGGAAGGTTATTAGTGTCTTGTAGTAAGAACCCCTTTCCTTCTAT
932285 CAATTTATTTCCTTTCTTCTTAAGCCAACCTTTTACCATCTATTTGTTCTTTTTTTCCTACCTAA
391 CAATTTATTTCCTTTCTTCTTAAGCCAACCTTTTACCATCTATTTGTTCTTTTTTTCCTACCTAA
932350 CCTCATTTTGTAGCAAACTCCTAAGCACCTTAT-TAGAAGGACTTGAGTTAGTACTTTTAGAACC
456 CCTCATTTTGTAGCAAACTCCTAAGCACCTTATAT-GAAGGACTTGAGTTAGTACTTTTAGAACC
932414 TAACCT
520 TAACCT
932420 CATTTCTTTAAAGCCTTTTTATTTCAGGAACACTTGCTGTCTTTCTAGGTCCTACAATCAAAGTG
1 CATTTCTTTAAAGCCTTTTTATTTCAGGAACACTTGCTGTCTTTCTAGGTCCTACAATCAAAGTG
932485 TAAGTCTTACCTCACCAAGTGGTGTAGGGCGTGCTTATATCATGTGGTAATCAGAACTAAGGTGG
66 TAAGTCTTACCTCACCAAGTGGTGTAGGGCGTGCTTATATCATGTGGTAATCAGAACTAAGGTGG
*
932550 AATGAAGCAAGTTATGAAGTGTTGAGTCATCGAAACAAGTAAAAACAAAAGGAAAAAGAAGT-TC
131 AAGGAAGCAAGTTATGAAGTGTTGAGTCATCGAAACAAGTAAAAACAAAAGGAAAAAGAAGTGT-
932614 TATTCAAAAATCCTTGAAGAAACGTGAAAAAAGAAAGCAAAAGGAAAGAAAAAATCAAAGCAAGA
195 TATTCAAAAATCCTTGAAGAAACGTGAAAAAAGAAAGCAAAAGGAAAGAAAAAATCAAAGCAAGA
*
932679 AAATAAAAGTTAAAAGCAAAGGTTGTTTCATACATGAACAAGTGCCAACAAGCCTAAAGTTGTTT
260 AAAGAAAAGTTAAAAGCAAAGGTTGTTTCATACATGAACAAGTGCCAACAAGCCTAAAGTTGTTT
*
932744 TCAACACTTTGATTATGGCTAGGGAAGGTTGTTAGTGTCTTGTAGTAAGAACCCCTTTCCTTCTA
325 TCAACACTTTGATTATGGCTAGGGAAGGTTATTAGTGTCTTGTAGTAAGAACCCCTTTCCTTCTA
932809 TCAATTTATTTCCTTTCTTCTTAAGCCAACCTTTTACCATCTATTTGTTCTTTTTTTCCTACCTA
390 TCAATTTATTTCCTTTCTTCTTAAGCCAACCTTTTACCATCTATTTGTTCTTTTTTTCCTACCTA
*
932874 ACCTCATTTTGTAGCAAACTCCTAAGCACCTTATATGAAGGACTTGAGTTAGTACTTTTAGAACT
455 ACCTCATTTTGTAGCAAACTCCTAAGCACCTTATATGAAGGACTTGAGTTAGTACTTTTAGAACC
932939 TAAC
520 TAAC
932943 AAGAGAGAAA
Statistics
Matches: 516, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
524 1 0.00
525 514 1.00
526 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (525 bp):
CATTTCTTTAAAGCCTTTTTATTTCAGGAACACTTGCTGTCTTTCTAGGTCCTACAATCAAAGTG
TAAGTCTTACCTCACCAAGTGGTGTAGGGCGTGCTTATATCATGTGGTAATCAGAACTAAGGTGG
AAGGAAGCAAGTTATGAAGTGTTGAGTCATCGAAACAAGTAAAAACAAAAGGAAAAAGAAGTGTT
ATTCAAAAATCCTTGAAGAAACGTGAAAAAAGAAAGCAAAAGGAAAGAAAAAATCAAAGCAAGAA
AAGAAAAGTTAAAAGCAAAGGTTGTTTCATACATGAACAAGTGCCAACAAGCCTAAAGTTGTTTT
CAACACTTTGATTATGGCTAGGGAAGGTTATTAGTGTCTTGTAGTAAGAACCCCTTTCCTTCTAT
CAATTTATTTCCTTTCTTCTTAAGCCAACCTTTTACCATCTATTTGTTCTTTTTTTCCTACCTAA
CCTCATTTTGTAGCAAACTCCTAAGCACCTTATATGAAGGACTTGAGTTAGTACTTTTAGAACCT
AACCT
Found at i:936824 original size:50 final size:50
Alignment explanation
Indices: 936719--936825 Score: 119
Period size: 50 Copynumber: 2.1 Consensus size: 50
936709 TCACACTCCA
* * * * *
936719 ATTTGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGT
1 ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACATATTATCGT
* *
936769 GTTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAG-GACATTATTCATC-T
1 ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACA-TATT-ATCGT
936819 ATTTTCC
1 ATTTTCC
936826 ACATATCCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
49 3 0.06
50 41 0.87
51 3 0.06
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (50 bp):
ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACATATTATCGT
Found at i:936947 original size:22 final size:22
Alignment explanation
Indices: 936922--936963 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
936912 CAATTCATTT
936922 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
936944 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
936964 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:941625 original size:22 final size:22
Alignment explanation
Indices: 941600--941641 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
941590 CAATTCATTT
941600 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
941622 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
941642 CCAGCACCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:947061 original size:16 final size:16
Alignment explanation
Indices: 947027--947087 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
947017 TGTAAGTATC
* *
947027 TTCATTTTCTTACTAT
1 TTCATTTCCTTATTAT
*
947043 TTCATTTCCTTATTCT
1 TTCATTTCCTTATTAT
*
947059 TTCATATT--TTCTTAT
1 TTCAT-TTCCTTATTAT
*
947074 TTCATTACCTTATT
1 TTCATTTCCTTATT
947088 CTTTTCTTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 1 0.03
15 10 0.29
16 22 0.63
17 2 0.06
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCATTTCCTTATTAT
Found at i:953965 original size:27 final size:26
Alignment explanation
Indices: 953913--953968 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
953903 TTTTTTGCTT
* *
953913 TTTCTTCTTTTGAGTGTTGGATTTTC
1 TTTCTTCTTTTGAGTGTTGCACTTTC
953939 TTTCTTTCTTTTGAGTGCTT-CACTTTC
1 TTTC-TTCTTTTGAGTG-TTGCACTTTC
953966 TTT
1 TTT
953969 TCTGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 20 0.77
28 2 0.08
ACGTcount: A:0.07, C:0.16, G:0.14, T:0.62
Consensus pattern (26 bp):
TTTCTTCTTTTGAGTGTTGCACTTTC
Found at i:958496 original size:24 final size:24
Alignment explanation
Indices: 958464--958511 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
958454 CTTCAAGTTA
* *
958464 AAGATTCAAGAAACATGTCTTTTG
1 AAGAATCAAGAAACATGACTTTTG
* *
958488 AAGAATCAATAAACGTGACTTTTG
1 AAGAATCAAGAAACATGACTTTTG
958512 GTGATCCACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (24 bp):
AAGAATCAAGAAACATGACTTTTG
Found at i:974745 original size:32 final size:33
Alignment explanation
Indices: 974684--974750 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
974674 TAAAAATTCA
974684 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATGGAATATGGATAG
974716 AAGAAAGGAAATGA-TAAGTAA-GGAA-ATGGATAG
1 AAGAAA-GAAATGATTAA--AATGGAATATGGATAG
974749 AA
1 AA
974751 ATGTTATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
32 14 0.45
33 15 0.48
34 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATGGAATATGGATAG
Found at i:974992 original size:36 final size:35
Alignment explanation
Indices: 974906--975005 Score: 128
Period size: 35 Copynumber: 2.8 Consensus size: 35
974896 TTATATAGGC
* * * **
974906 GTGAAATGGTGATAGAAGATGGTAATGATATAGGT
1 GTGAAATGGTGATGGAAGATGGTGATGTTATAGAA
* *
974941 GTGCAATGGTAATGGAAGATGGTGATGTTATAGAA
1 GTGAAATGGTGATGGAAGATGGTGATGTTATAGAA
974976 GTGAAAATGGTGATGGAAGATGGTGATGTT
1 GTG-AAATGGTGATGGAAGATGGTGATGTT
975006 TAGGTAGTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
35 31 0.56
36 24 0.44
ACGTcount: A:0.34, C:0.01, G:0.36, T:0.29
Consensus pattern (35 bp):
GTGAAATGGTGATGGAAGATGGTGATGTTATAGAA
Found at i:980554 original size:130 final size:130
Alignment explanation
Indices: 980407--980654 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
980397 ATTATTTATA
*
980407 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* *
980472 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
980537 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
980602 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
980655 GAAGAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:980685 original size:130 final size:129
Alignment explanation
Indices: 980421--980685 Score: 318
Period size: 130 Copynumber: 2.0 Consensus size: 129
980411 ATTTGGTCCT
* *
980421 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
980486 TGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
980551 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
980616 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
980680 -A
128 CA
980681 AAATT
1 AAATT
980686 TGGGTCTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 101 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:981013 original size:28 final size:27
Alignment explanation
Indices: 980982--981044 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
980972 AGTTGATACA
*
980982 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
981010 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
981038 ATATTTT
1 ATATTTT
981045 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:981145 original size:16 final size:18
Alignment explanation
Indices: 981124--981157 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
981114 ATTTCTTATT
981124 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
981140 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
981158 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:981304 original size:21 final size:21
Alignment explanation
Indices: 981280--981322 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
981270 TATTACCTTA
981280 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
981301 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
981322 A
1 A
981323 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:981340 original size:35 final size:35
Alignment explanation
Indices: 981291--981376 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
981281 ATTGAAGTAT
** * *
981291 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* *
981326 TTTAGAATAAAATTGAATTACTTTGGAAATTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
981361 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
981377 TGACTGTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:998214 original size:20 final size:21
Alignment explanation
Indices: 998191--998230 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
998181 TGCTTTCTCT
998191 TTTTTGAATTTT-TTTTCTTC
1 TTTTTGAATTTTCTTTTCTTC
**
998211 TTTTTGTCTTTTCTTTTCTT
1 TTTTTGAATTTTCTTTTCTT
998231 TTTGCACTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTTGAATTTTCTTTTCTTC
Found at i:1001665 original size:24 final size:25
Alignment explanation
Indices: 1001638--1001689 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
1001628 AAGAAAAATC
* *
1001638 AGAAAAG-AAAGTGAAGCACTCAAA
1 AGAAAAGAAAAATCAAGCACTCAAA
*
1001662 AG-AAAGAAAAATCCAGCACTCAAA
1 AGAAAAGAAAAATCAAGCACTCAAA
1001686 AGAA
1 AGAA
1001690 GAAAAAGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 4 0.17
24 18 0.78
25 1 0.04
ACGTcount: A:0.60, C:0.15, G:0.17, T:0.08
Consensus pattern (25 bp):
AGAAAAGAAAAATCAAGCACTCAAA
Found at i:1007012 original size:12 final size:13
Alignment explanation
Indices: 1006995--1007025 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1006985 AATTATATAT
1006995 ATGAAAT-AAGAA
1 ATGAAATAAAGAA
1007007 ATGAAATAAAGAA
1 ATGAAATAAAGAA
1007020 ATGAAA
1 ATGAAA
1007026 AGATAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
ATGAAATAAAGAA
Found at i:1024961 original size:26 final size:26
Alignment explanation
Indices: 1024932--1024986 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
1024922 TAGGGTCTAA
*
1024932 AAATGGTAATGATAGGGGTAGGATAG
1 AAATGATAATGATAGGGGTAGGATAG
* *
1024958 AAATGATTATGATAGGGTTAGGATAG
1 AAATGATAATGATAGGGGTAGGATAG
1024984 AAA
1 AAA
1024987 AGGTTAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.25
Consensus pattern (26 bp):
AAATGATAATGATAGGGGTAGGATAG
Found at i:1025270 original size:6 final size:6
Alignment explanation
Indices: 1025259--1025302 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
1025249 GATGTAGGAG
*
1025259 TCTTTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
1025303 TGTTGCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:1025282 original size:12 final size:12
Alignment explanation
Indices: 1025259--1025302 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
1025249 GATGTAGGAG
1025259 TCTTTTTC-TTT
1 TCTTTTTCTTTT
*
1025270 TCTTTTTGTTTT
1 TCTTTTTCTTTT
1025282 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
1025295 TCTCTTTT
1 TCT-TTTT
1025303 TGTTGCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 7 0.25
13 13 0.46
14 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:1025538 original size:32 final size:33
Alignment explanation
Indices: 1025477--1025543 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
1025467 TAAAAATTCA
1025477 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATGGAATATGGATAG
1025509 AAGAAAGGAAATGA-TAAGTAA-GGAA-ATGGATAG
1 AAGAAA-GAAATGATTAA--AATGGAATATGGATAG
1025542 AA
1 AA
1025544 ATGTTATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
32 14 0.45
33 15 0.48
34 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATGGAATATGGATAG
Found at i:1025794 original size:36 final size:35
Alignment explanation
Indices: 1025687--1025801 Score: 124
Period size: 35 Copynumber: 3.3 Consensus size: 35
1025677 AGGGATTGGT
* * *
1025687 TGTTAATAGGTGTGAAATGGTGATAGAAGATGGTAA
1 TGTT-ATAGGCGTGAAATGGTGATGGAAGATGGTGA
* * * * *
1025723 TGATATAGGCGTGCAATGGTAATGTAAGATAGTGA
1 TGTTATAGGCGTGAAATGGTGATGGAAGATGGTGA
*
1025758 TGTTATAGGCGTGAAAATGGTGATGGAGGATGGTGA
1 TGTTATAGGCGTG-AAATGGTGATGGAAGATGGTGA
1025794 TGTT-TAGG
1 TGTTATAGG
1025802 TAGTATCTTA
Statistics
Matches: 64, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
35 40 0.62
36 24 0.38
ACGTcount: A:0.31, C:0.03, G:0.36, T:0.30
Consensus pattern (35 bp):
TGTTATAGGCGTGAAATGGTGATGGAAGATGGTGA
Found at i:1032490 original size:15 final size:15
Alignment explanation
Indices: 1032470--1032509 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1032460 TGAGGCTTCT
*
1032470 GATGCCACTTGATGC
1 GATGCCACTTAATGC
1032485 GATGCCACTTAATGC
1 GATGCCACTTAATGC
*
1032500 AATG-CACTTA
1 GATGCCACTTA
1032510 TACCTCTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (15 bp):
GATGCCACTTAATGC
Found at i:1039011 original size:12 final size:13
Alignment explanation
Indices: 1038994--1039024 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1038984 AATTATATAT
1038994 ATGAAAT-AAGAA
1 ATGAAATAAAGAA
1039006 ATGAAATAAAGAA
1 ATGAAATAAAGAA
1039019 ATGAAA
1 ATGAAA
1039025 GGATAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
ATGAAATAAAGAA
Found at i:1041380 original size:24 final size:24
Alignment explanation
Indices: 1041353--1041398 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1041343 AATGTCAACA
1041353 GACACAACTCTTGGAAATTCAAGT
1 GACACAACTCTTGGAAATTCAAGT
*** *
1041377 GACATTTCTCTTGGAACTTCAA
1 GACACAACTCTTGGAAATTCAA
1041399 ACGACATTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (24 bp):
GACACAACTCTTGGAAATTCAAGT
Found at i:1041404 original size:24 final size:24
Alignment explanation
Indices: 1041360--1041406 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1041350 ACAGACACAA
**
1041360 CTCTTGGAAATTCAAGTGACATTT
1 CTCTTGGAAATTCAAACGACATTT
*
1041384 CTCTTGGAACTTCAAACGACATT
1 CTCTTGGAAATTCAAACGACATT
1041407 ATCTTTGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (24 bp):
CTCTTGGAAATTCAAACGACATTT
Found at i:1041422 original size:24 final size:24
Alignment explanation
Indices: 1041377--1041422 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1041367 AAATTCAAGT
* *
1041377 GACATTTCTCTTGGAACTTCAAAC
1 GACATTTCTCTTGAAACATCAAAC
1041401 GACATTATCT-TTGAAACATCAA
1 GACATT-TCTCTTGAAACATCAA
1041423 GAGATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (24 bp):
GACATTTCTCTTGAAACATCAAAC
Found at i:1042768 original size:13 final size:13
Alignment explanation
Indices: 1042746--1042775 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1042736 GATGTAGGAG
*
1042746 TCTTTTTTTTTCT
1 TCTTTCTTTTTCT
1042759 TCTTTCTTTTTCT
1 TCTTTCTTTTTCT
1042772 TCTT
1 TCTT
1042776 GTTGCAGCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TCTTTCTTTTTCT
Found at i:1042974 original size:12 final size:13
Alignment explanation
Indices: 1042957--1042987 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1042947 AATTATATAT
1042957 ATGAAAT-AAGAA
1 ATGAAATAAAGAA
1042969 ATGAAATAAAGAA
1 ATGAAATAAAGAA
1042982 ATGAAA
1 ATGAAA
1042988 GGATAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
ATGAAATAAAGAA
Found at i:1048498 original size:17 final size:17
Alignment explanation
Indices: 1048476--1048509 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1048466 GCAAGGAAAT
1048476 GAACCAACATGTTCACA
1 GAACCAACATGTTCACA
1048493 GAACCAACATGTTCACA
1 GAACCAACATGTTCACA
1048510 TCAAGAGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.12, T:0.18
Consensus pattern (17 bp):
GAACCAACATGTTCACA
Found at i:1051669 original size:22 final size:22
Alignment explanation
Indices: 1051617--1051662 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1051607 CACTTGAAGT
*
1051617 GCAACAAGTTGTGATCATTGAG
1 GCAACAAGTTGTGATCATTAAG
1051639 GCAACAAGTTGTGATCATTAAG
1 GCAACAAGTTGTGATCATTAAG
1051661 GC
1 GC
1051663 TCCAAGTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (22 bp):
GCAACAAGTTGTGATCATTAAG
Found at i:1052098 original size:17 final size:18
Alignment explanation
Indices: 1052062--1052097 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1052052 GGAGTAAGAG
*
1052062 TGAAAAGATACAATATTT
1 TGAAAAGATACAACATTT
*
1052080 TGAAAGGATACAACATTT
1 TGAAAAGATACAACATTT
1052098 GGAGTACAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (18 bp):
TGAAAAGATACAACATTT
Found at i:1058470 original size:20 final size:20
Alignment explanation
Indices: 1058445--1058495 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1058435 GGCCAAGAGC
*
1058445 ATGTATCTTCATAAAAAATA
1 ATGTATTTTCATAAAAAATA
*
1058465 ATGTATTTTCATCAAAAATA
1 ATGTATTTTCATAAAAAATA
1058485 ATGTATTTTCA
1 ATGTATTTTCA
1058496 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (20 bp):
ATGTATTTTCATAAAAAATA
Found at i:1065609 original size:2 final size:2
Alignment explanation
Indices: 1065602--1065626 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1065592 ATCATCAACT
1065602 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1065627 TCAGCTACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1074550 original size:23 final size:22
Alignment explanation
Indices: 1074521--1074563 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1074511 GGCTCATTCT
1074521 TTTGAATT-TCAAGAGGTACATCC
1 TTTGAATTGTCAA-AGG-ACATCC
1074544 TTTGAATTGTCAAAGGACAT
1 TTTGAATTGTCAAAGGACAT
1074564 ATCCTGTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (22 bp):
TTTGAATTGTCAAAGGACATCC
Found at i:1075790 original size:14 final size:13
Alignment explanation
Indices: 1075771--1075804 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1075761 GTGCTTCAAC
1075771 TTTCTTTCTTTCTT
1 TTTCTTTCTTT-TT
1075785 TTTCTTTCTTTTT
1 TTTCTTTCTTTTT
*
1075798 CTTCTTT
1 TTTCTTT
1075805 TTTAGTGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTCTTTTT
Done.